Here's a place where I can post my thoughts on new papers, provide updates on my projects, and post info that will eventually be on my website The Theropod Database - http://theropoddatabase.com/ . It will center on theropods, but may delve into other topics as well such as phylogenetics.

Tuesday, May 8, 2018

Cau's 2018 theropod tree

Hi all. Work's been rapid on the Ornithoscelida project, which has improved due to David Marjanovic's request that I provide a citation for each character state we think was inaccurately coded by Baron et al.. It's time consuming, but has revealed several times where I was mistaken in my scoring, and forces you to really evaluate whether you think the evidence is good enough to truly call someone's character state choice wrong. As tedious as it is, this should really become the standard for scoring justification in any analysis (and no, I didn't do that for the Lori analysis, though I have the preliminary steps for a far future offshoot of it).

Speaking of the Ornithoscelida paper, coauthor and fellow theropod blogger Andrea Cau just got a big new paper published using his MegaMatrix character list. So congrats! It's a summary of theropod evolution focusing on the path from Teleocrater to Meleagris, detailing the changes in each node from Pan-Aves (well, technically that's a stem) to Aves, and using that data to examine the trends and rates of change along that line. We get two new clade names as well. Dracohors is (Megalosaurus bucklandii < - Marasuchus lilloensis), so covers silesaurs and dinosaurs. The use of a stem instead of a node like Silesaurus+Megalosaurus was wise considering some analyses (especially those recovering ornithischian silesaurids) recover Lewisuchus and such at an uncertain position relative to Silesauridae, but it's always closer to dinosaurs than Marasuchus. But come on, 'Dracohors'? Dragonian prostitutes? Did no one learn from Ascendonanus?! Oh, and the plural is 'dracohorsians', which sounds like a hybrid race from My Little Pony. Maniraptoromorpha is (Vultur gryphus < - Tyrannosaurus rex) and is a sorely needed name that I could have used in the Lori paper, since we ended up limiting the taxon sample to maniraptoromorphs. Recall that the results of TWG characters get worse as you get further from Norell et al.'s (2001) or Clarke's (2002) original scopes, and I didn't want to be Petersian and tackle e.g. the Megaraptora problem without the Carrano et al. (2012) or Novas et al. (2013) characters while using a batch of maniraptoromorph characters. The name Maniraptoromorpha also fits the -morpha > -formes > basic clade pattern, which I like.

Sacrum of the maniraptoromorph Bambiraptor feinbergi (holotype AMNH 30556) in ventral view, anterior to left (courtesy of the AMNH).

Cau's analysis itself has positives and negatives. What everyone knows about the MegaMatrix is that it's HUGE. I'm talking 1781 characters. That's more than all Mesozoic theropod analyses except the poorly coded Livezey and Zusi (2007), which used 2954 characters and focused on living birds though technically included 30 non-avian theropods too. But if you look at the matrix, the size is a tiny bit misleading because Cau doesn't use any multistate characters. So instead of a single character of "Premaxilla - number of teeth - three or less (0); four (1); five (2); six (3); seven or more (4)", he has-
"14): Premaxilla, fifth alveolus: absent (0); present (1). ...
1717): Premaxilla, sixth alveolus: absent (0); present (1).
1718): Premaxilla, seventh alveolus: absent (0); present (1).
1759): Premaxilla, fourth alveolus: absent (0); present (1)."
Or instead of "Sacral vertebrae - number - two or less (0); three (1); four (2); five (3); six (4); seven (5); eight (6); nine (7); ten (8); eleven or more (9)", he has-
"343): Third sacral vertebra: absent (0); present (1). ...
1707): Fourth sacral vertebra: absent (0); present (1).
1708): Fifth sacral vertebra: absent (0); present (1).
1709): Sixth sacral vertebra: absent (0); present (1).
1710): Seventh sacral vertebra: absent (0); present (1).
1711): Eight sacral vertebra: absent (0); present (1).
1712): Ninth sacral vertebra: absent (0); present (1).
1713): Tenth sacral vertebra: absent (0); present (1).
1714): Eleventh sacral vertebra: absent (0); present (1)."
Now this is largely fine, as both ordered and unordered multistate characters can generally be scored this way using certain procedures to avoid weighting. Cau does it to make Bayesian analyses easier (pers. comm.). But the Lori character list would be 25% longer (875 non-zero states in my 700 characters) using this method, for instance. Of course the MegaMatrix was designed for a larger taxonomic scope, so will necessarily have more characters, those meant for carnosaurs, ceratosaurs, basal dinosauromorph phylogeny, etc.. Limiting the taxon sample to maniraptoromorphs finds 1170 parsimony-informative characters in Cau's dataset. There are also 14 parsimony-uninformative characters in the Lori dataset, since some TWG characters were designed for tyrannosauroids or positioning outgroups like Dilophosaurus, Monolophosaurus, etc.. This would leave 861 Cau-style characters in the Lori analysis, so 74% as many as the MegaMatrix. Not so bad...

It also doesn't use any polymorphic scoring, so there are no 0+1 scores in Cau's matrix. I'm not sure if this matters analytically, since I assume he scores a polymorphic taxon unknown, and I don't know how TNT treats polymorphies when it's making trees. Not that the standard method is without its problems, since TNT is stupider than PAUP in treating uncertainty polymorphies (could have either four or five teeth) the same as actual polymorphies (some have four teeth, others five). He also doesn't differentiate inapplicable (-) and unknown (?) scorings, which is fine functionally as I believe TNT treats them the same, but this and the lack of polymorphic scores do make the matrix itself more opaque to users since a lot of question marks there aren't technically unknown. For the Lori matrix, we're providing both a TNT and a NEXUS file, with the latter showing uncertainty polymorphies vs. actual polymorphies, plus when taxa can but shouldn't be scored due to ontogeny (e.g. a juvenile with unfused bones, when adults are unknown).

Cranial elements of the maniraptoromorph Microvenator celer (holotype AMNH 3041), with supposed right lacrimal of Makovicky and Sues in lateral view (upper left, anterior to right), dentary in dorsal view (lower right, anterior to top) and unidentified elements (scale bar in cm) (courtesy of the AMNH).

The taxon sample is interesting because it is very reduced compared to the Halszkaraptor analysis (Cau et al., 2017) that used the same character list (plus eight new characters; though among maniraptoromorphs, Jianianhualong and Chongmingia were added). Alvarezsaurids are only represented by Alvarezsaurus and Patagonykus, caenagnathoids by Anzu and Khaan, therizinosaurs by Beipiaosaurus and Falcarius (and Jianchangosaurus... see below), etc.. Which still leaves it as the best large scale Mesozoic theropod analysis published, but without e.g. undisputed alvarezsaur skulls (since Haplocheirus finds itself elsewhere in some analyses), it's bound to get things wrong. And it does differ from Cau et al.'s 2017 trees which focused on maniraptoromorphs. Zuolong is outside Neotetanurae instead of a coelurosaur, Coelurus is a maniraptoromorph [see how useful this clade name is!] instead of a tyrannosauroid, Jianchangosaurus is an alvarezsaur(!), therizinosaurs are caenagnathiforms instead of outside Pennaraptora, Fukuivenator is a paravian instead of a therizinosaur, halszkaraptorines are unenlagiines, Xiaotingia is a scansoriopterygid instead of an anchiornithid, scansoriopterygids are further from Aves than Archaeopteryx, and Zhongjianornis is in Fake Ornithuromorpha instead of sister to Pygostylia. Cau states on page 4 that taxon choice was based on a subjective (or at least not objectively justified) "balanced series of criteria" and I get that the point of the paper is trends leading to Aves, but having the quite complete Jianchangosaurus as the first branching of four alvarezsaurs, and eliminating a major step by placing therizinosaurs sister to oviraptorosaurs, seem like problems. I'm sure the main trends are only very minorly affected, but still. I think if I needed a reduced taxon sample (which was a real concern during part of the Lori process...) and was being subjective anyway, I would fiddle with the sample until I got a topology that matched the full analysis. Or maybe Jianianhualong, Chongmingia and/or the added eight characters changed the topology, and this whole paragraph is misled. Or maybe the reduced outgroup in the Halszkaraptor matrix affected the topology (only eight non-maniraptoromorphs compared to 58 here), which would be problematic for coelurosaur analyses since most have just been using 2-5 of the same outgroup taxa (Sinraptor dongi, Allosaurus, Monolophosaurus, Dilophosaurus, and/or Coelophysis...)..

What of the phylogenetic results themselves? Eodromaeus and herrerasaurs are in an unresolved polytomy with sauropodomorphs and ornithoscelidans, which matches their increasingly uncertain position now that people are using large taxon samples for more than Nesbitt-derived matrices and Sereno's non-testing 'analyses' from the 90s are fading into history. Ornithoscelida itself is recovered, but with only Heterodontosaurus and Tianyulong representing Ornithischia, I don't give that much credit regardless of the character count. Heterodontosaurids are very theropody in some ways few other ornithischians are and generally fall out as the first branching clade in analyses (now that Pisanosaurus is a silesaurid, which Cau also recovers) and ignoring Chilesaurus for the moment. But I'm co-writing a whole paper on that, so let's move on to theropods. Cryolophosaurus is a dilophosaurid coelophysoid, which is counter the recent consensus of finding it closer to averostrans or even a tetanurine itself. As stated above, Zuolong is outside Neotetanurae, which is weird since it generally falls out as a basal coelurosaur. Chilesaurus is also here, matching its authors' conclusion, but I think the poor ornithischian sample keeps this analysis from adequately dismissing an ornithischian identity. But I'm co-writing a paper on that and etc. etc.. Back to theropods. Cau recovers a Rauhut-like Carnosauria including megalosaurids, piatnitzkysaurids, Monolophosaurus and allosaurs. Neovenator is sister to Allosaurus and Sinraptor sister to Acrocanthosaurus among the latter, which harkens back to late 90s phylogenies. Megaraptorans (including Gualicho) are tyrannosauroids closer to Tyrannosaurus than Eotyrannus, matching Novas et al. (2013). The tree is untraditional in placing compsognathid-grade taxa outside Tyrannoraptora, though Novas had that opinion back in the early 1990s. As stated above, the maniraptoran section has the out of vogue caenagnathiform therizinosaurs and the very weird alvarezsauroid Jianchangosaurus, but those might be glitches due to the taxon sample. Fukuivenator is sometimes a dromaeosaurid and sometimes the basalmost paravian, which its authors recovered with the addition of three steps. Cau finds avialan troodontids, standard for his published analyses. Like his Halszkaraptor version, Rahonavis is close to jeholornithids and Protopteryx can be outside Ornithothoraces (it always is in the 2017 trees). The latter is funny because I had that idea way back in 2000 on the DML ("My analysis of 31 characters and 6 taxa resulted in a single most parsimonious teee (CI .81, HI .19, RI .78)" ... how quaint), so if it turns out to be true that would be something. Finally, presumably due to excluding fragmentary taxa like Teviornis, the huge ornithuromorph polytomy of the 2017 paper is resolved and Patagopteryx falls out by Apsaravis, Ichthyornis and Hesperornis+Aves. Wha?

Interestingly, Cau also performed a Bayesian analysis. In these, herrerasaurs are sister to Dinosauria like Baron and Williams (2018), but Eodromaeus is a basal ornithoscelidan. Allosauroid relationships now match the Carrano et al. consensus, and Zuolong is a basal coelurosaur but Chilesaurus follows it. Gualicho is now closer to tyrannosaurids than to megaraptorans. Jianchangosaurus is back to being a therizinosaur, but Ornitholestes and Haplocheirus are basal ornithomimosaurs. Weird. Therizinosaurs are no longer sister to oviraptorosaurs, and actually move down an extra node to be stemward of alvarezsaurids too. Especially interesting is that scansoriopterygids move way down from being avialans to being basal oviraptorosaurs. Are they the missing Jurassic oviraptorosaurs? This lets Xiaotingia go back to Anchiornithidae. Rahonavis is now sister to Jeholornithidae instead of a couple nodes stemward of it, and Sapeornis is a confuciusornithiform. Protopteryx is always an enantiornithine (aw...), but Patagopteryx is still way crownward, though now Vorona joins it (basal fake ornithuromorph in the parsimony analysis). Well, that does match their Late Cretaceous age at least. Considering all of these changes, I like a few things better about the parsimony version and a few things better about the Bayesian version.

How does Cau's Maniraptoromorpha topology compare to Lori's? Quite different on both a broad level and with regard to the detailed relationships within the clades, although there are a few things that aren't common but popped up in both. I'm dying to say more, but that post has got to wait. Congrats again to Andrea.

References- Norell, Clark and
Makovicky, 2001. Phylogenetic relationships among coelurosaurian theropods. In
Gauthier and Gall (eds.). New Perspectives on the Origin and Early Evolution of
Birds: Proceedings of the International Symposium in Honor of John H. Ostrom.
49-67.

Clarke, 2002. The morphology and systematic position of Ichthyornis
Marsh and the phylogenetic relationships of basal Ornithurae. PhD thesis, Yale University.
532 pp.

Baron and Williams, 2018. A re-evaluation of the enigmatic dinosauriform Caseosaurus crosbyensis from the Late Triassic of Texas, USA and its implications for early dinosaur evolution. Acta Palaeontologica Polonica. 63(1), 129-145.

38 comments:

@"But come on, 'Dracohors'? Dragonian prostitutes? Did no one learn from Ascendonanus?!"

Sorry for the bizarre meaning some of you may read there, but the term is a combination of Latin words, not English. So, I see no reason to disagree with a name just because in your mother language it sounds weird.There are a lot of English terms that sound wery weird or funny for an Italian reader, but this is not a reason for not using them.Unfortunately, I am not that inside English prostitution terminology for knowing that meaning. ;-)

In TNT "0/1" in binary characters is the same as "?", so the reason for scoring them just as unknown states.

The "Patagopterygiform-Carinatae" clade results even after updating Ichthyornis and Confuciusornis (so, in my matrix versions done after this manuscript was submitted), so I am confident it represents a plausible avialan clade. In particular, I am intriguied that it is stratigraphically consistent and results even in the parsimony analysis not using stratigraphic data.

Erlikosaurus was confusingly described as gen. et sp. nov. in both Barsbold and Perle (1980) and Perle (1981), though the former attributes the name to Perle only. Perle (1981) spelled the genus name Erlicosaurus, which has been followed by some authors (e.g. Barsbold, 1983; Clark et al., 1994). However, according to the ICZN (Article 32.5), since there is no evidence in the original publication that the name is spelled incorrectly, and the issue is not with suffix or gender, Erlikosaurus is the correct original spelling. This makes Erlicosaurus an unjustified emendation (Article 33.2), since there is no evidence in Perle (1981) that he purposefully changed the spelling, and the original spelling is not cited. According to Article 33.2.3, "the name thus emended is available and it has its own author and date and is a junior objective synonym of the name in its original spelling." An unjustified emendation can become justified it it has prevailing usage and is attributed the the original author and date, but Erlikosaurus has 23,700 Google hits vs. 1,450 for Erlicosaurus, and 232 vs. 104 Google Scholar hits. Thus the genus should be spelled Erlikosaurus.

...What's wrong with Ascendonanus? I've been playing with possible English pronunciations of it for minutes and haven't found anything.

Oh, and the plural is 'dracohorsians'

Of course it's "dracohortians", seeing as cohors is cohort-s plus the Latin (and Greek etc.) rule that turns every -ts into -s.

The name Maniraptoromorpha also fits the -morpha > -formes > basic clade pattern, which I like.

Seconded.

I'm talking 1781 characters.

...of which 350 are parsimony-uninformative. However, they aren't constant characters, even though the Bayesian analysis was not set to expect the absence of constant characters. That could have distorted its results.

Livezey and Zusi (2007), which used 2954 characters

...of which several hundred were parsimony-uninformative.

Cau does it to make Bayesian analyses easier (pers. comm.).

I don't understand that. MrBayes has no trouble dealing with both ordered and unordered multistate characters (pers. obs.). Stepmatrices are what it can't deal with.

Not that the standard method is without its problems, since TNT is stupider than PAUP in treating uncertainty polymorphies (could have either four or five teeth) the same as actual polymorphies (some have four teeth, others five).

PAUP* does it the same way by default. You have to tell it pset mstaxa=variable if you want it to treat polymorphism differently from partial uncertainty. (The only difference is in the length of the resulting trees, not their topology: PAUP* can't reconstruct ancestors as polymorphic, so polymorphic OTUs get extra steps on their terminal branches.)

He also doesn't differentiate inapplicable (-) and unknown (?) scorings, which is fine functionally as I believe TNT treats them the same

The sign - doesn't mean "inapplicable" at all as far as PAUP* is concerned. It means "gap in a molecular sequence". The default setting is to treat gaps as unknown, but make sure not to use the other setting, which is to treat them as a 5th base/21st amino acid.

and Protopteryx can be outside Ornithothoraces (it always is in the 2017 trees). The latter is funny because I had that idea way back in 2000 on the DML

That struck me immediately :-)

Especially interesting is that scansoriopterygids move way down from being avialans to being basal oviraptorosaurs. Are they the missing Jurassic oviraptorosaurs?

!!!

Oviraptorosaurs as secondarily non-arboreal like some kinda mammal...!!!

"...What's wrong with Ascendonanus? I've been playing with possible English pronunciations of it for minutes and haven't found anything."

You need to get your mind in the gutter, David. ;) Dann Pigdon mentioned it first on the DML- http://dml.cmnh.org/2017Nov/msg00077.html

"The sign - doesn't mean "inapplicable" at all as far as PAUP* is concerned. It means "gap in a molecular sequence"."

Isn't that basically the molecular equivalent of inapplicable in a phenotypic context? The homologous portion of the sequence is not present, creating a 'gap' in describing its code just as if the homologous structure (e.g. teeth) isn't present, creating a 'gap' in describing its morphology.

"dracohorsian" is an English vernacular: I assume the plural is "dracohorsians". There is no Latin/Greek name "Dracohortes".

First, I performed analyses in BEAST, not MrBayes, and for epistemological reasons I have preferred to re-define all my characters as binary.

There is no reason for considering oviraptorosaurs as secondarily non-arboreal (SNA) in those scenarios having scansoriopterygids as their sister. SNA may be plausible if oviraptorosaurs result nested in Avialae, not if scansoriopterygids are removed from Paraves.

The idea that scansoriopterygians are basal oviraptorosaurs--given the former's unique flying apparatus (assuming that's correct)--could lead to some interesting revisions in how we restore the latter!

I see no reason to change much scansoriopterygid overall reconstruction just because they are closer to oviraptorosaurs than to avialans. A recontruction should be first based on direct evidence of the fossils. An in any case, what would differ in their morphology once placed as non-paravian pennaraptorans?

Since I am a huge paleontology nerd, I was curious if you could provide me with assistance for a list I am making of geologic time. There are many theropods I have trouble pinning down to a specific substage, so I came to you for help. If you are interested, I'll add you into the list of people who can edit it.

That's what The Theropod Database is for. If I don't have anything more specific there, then either I'm unaware of any more specific age, the sediments have not been dated more specifically or the exact locality is unknown. As with everything on the Database, I haven't updated it with papers from the past year due to working on Lori and Ornithoscelida.

Just updated my complete data matrix including Lesothosaurus.Once Lesothosaurus is included in the reduced matrix used in this 2018 paper, the result is so unexpected that I prefer not to mention it...

"this should really become the standard for scoring justification in any analysis"Of course! And so should never ignoring a character or taxon from a previous analysis unless you come up with an explicit reason for doing so. Ignoring previous characters and taxa has led to the impossibility of knowing whether the differences between the most recent analysis and the previous one are due to subjective selection of characters and taxa or to some real improvement in knowledge (I'm not picking on Andrea, this problem is ubiquitous...).

For the Lori analysis I specifically used every TWG character proposed through 2012 (except the new ones in Senter 2011, because that was published in a baraminology study and the DML bans any mention of creationism, so I didn't learn about its existence until too late). Each character I didn't use is listed with an explanation why. I aimed to use every named maniraptoromorph known from more than teeth or single elements (and used a lot of unnamed and single-element specimens too) and described the twenty exceptions. But I just learned yesterday of a taxon that slipped under the radar and should have been included but was not. That'll be the topic of a future post...

Micke yTo be honest, you will have a chance to incorporate anything you realized that you missed (such as Senter 2011 and the mystery missing taxon) because you and your coauthors will get your manuscript back for revisions before it is published, and you may make modifications that weren't brought up during peer review as long as you justify them (usually in the letter to the editor once you submit the revised version).

Eh, at some point any analysis has to decide on a cut-off point and proceed with the results and conclusions of that data. Adding taxa and/or characters would change the topology and constraint numbers even if the general results or Lori's placement were the same. Then we'd need to rewrite those portions and make new figures, etc.. I might use your advice to mention Corythoraptor's absence though (the missing taxon). Scott and I have another paper planned that will at least update the matrix with the missing taxa, the new Archaeopteryx, confuciusornithid and Ichthyornis skull data, etc..

MickeyIt's great to know of the other paper that will have an updated matrix. I know it's tough to reanalyze and potentially rewrite whole sections, but it's also frustrating for readers to read a paper that is already known to have an obsolete topology even before it's printed. But there is no practical solution (except to wait for the next paper with the updated matrix)...The parts of the trees that are identical or nearly identical in the two consecutive topologies will be able to be viewed as "more robust" than the variable parts.

It's an interesting dilemma. On the one hand, you could be extremely opaque like most papers are- don't explain why you didn't add some taxa or characters, don't mention the specimens or photos you had access to, don't hint at papers that existed in the time frame between running the analysis and submitting the paper, etc.. Or you could be open and transparent about exactly which data you included and why, and what data could help in the future, and an irrational reader could then be upset you didn't include that information. But no one ever complains that e.g. Brusatte et al. (2014) didn't include Senter's (2007) characters, even though that paper's in their reference list, because they never even hint at past TWG analyses they didn't incorporate. So readers are content because they aren't presented with the truth. I'd rather be up front about everything because I view the Lori analysis as one step in a process, and want to facilitate helping that process along. So don't be frustrated to know the Lori analysis is being updated, be frustrated that every other published analysis could have been updated prior to publication but those authors decided to keep you in the dark about it.

It's not "tough" to reanalyze the matrix and rewrite, it's just time consuming. If I get it scored to the current literature on 1-15, then see on 1-26 that Buitreraptor's holotype was redescribed it takes a week to rescore and run, then wait we have Eogranivora on 2-4 to score and run another week, but during that there's also the new Archaeopteryx paper by Rauhut et al. on 2-5, then Guo et al. on new Anchiornis on 2-10 and take a week to rescore and run that, etc.. Papers come out faster than the publishing cycle, so you have to choose one cut off point and use that or else nothing will ever get published.

That "always" is not appropriate: a MCCT of a Bayesian analysis is not a strict consensus. It is a single tree of those sampled in the analysis, the one with the highest sum of posterior probability. So, the "always" adverb is inappropriate there.What I omitted (for space limitations) was to include a half-compact tree of the Bayesian sample, which is the "Bayesian analogous" of the majority rule consensus tree. Given that the basalmost enantiornithine node in Fig.6 shows a very low pp, I suspect that Protopteryx should form an unresolved polytomy in the half-compact tree.

... last sentence in my previous comment is not complete.I meant: Given that the basalmost enantiornithine node in Fig.6 shows a very low pp, I suspect that Protopteryx should form an unresolved polytomy with the main ornithothoracine lineages in the half-compact tree